Comparative genomic hybridization (CGH) and location analysis are important applications which allow scientists to make biological measurements involving genomics and study expression and regulation of genes in biological systems. Both CGH and location analysis entail quantifying or measuring changes in copy number of genomic sequences in biological or medical samples. Recently, cDNA microarrays and oligo microarrays have been used for CGH studies. An oligo-array based approach has several substantial advantages over other technologies, in that it allows the designer to position the probes anywhere within the genomic or polynucleotide sequence of interest and to select those sequences in such a way as to optimize their informativity and their performance. Oligo probes can be placed at any set of loci or positioned to span any genomic intervals of interest at whatever density is commensurate with the real-estate or area available on the microarray (in terms of number of features). The copy numbers of DNA over the genomic regions of interest can be evaluated by analyzing the hybridization of target sequences to the surface-bound probes. The oligonucleotide probe approach also offers the flexibility of focusing in on regions within exons or introns of expressed sequences, including pre-micro RNAs or intergenic regions and regulatory regions for location analysis, as well as any desirable admixture of the aforementioned.
Allele-specific copy number measurements are of increasing importance to the research community for the diagnosis of disease, especially in cytogenetics and cancer. Methods for the accurate detection of alleles and quantitation of their respective copy numbers allow the screening of many distinct candidate polymorphisms in the amount of time it would take to analyze a single polymorphism individually. Rapid assessment of single nucleotide polymorphisms (SNPs) using restriction fragment length polymorphism (RFLP) and allele-specific fluorophores have already been developed but typically require amplification through methods like PCR, and are not high throughput. Development of high throughput means for analyzing SNPs and allelic copy number would be beneficial.